AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i207_holliday_junction_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0244 300 tRNA-guanine transglycosylase (tgt) #2 HI0245 123 queuosine biosynthesis protein (queA) #3 HI0313 62 Holliday junction DNA helicase (ruvA) #4 HI0314 46 crossover junction endodeoxyribonuclease (ruvC) #5 HI0315 159 conserved hypothetical protein Motif number 1 GAATAATGATGACCAACTTAATCATAAATTTAGTC 1 85 1 GACATTATCT 0.959374 -216 ATAAATTTAGTCATATTTTTATCCTTAGTATGATT 1 108 1 TCTATTATCT 0.829331 -193 CGTAGATCCTGAGTTTGTTAATCATACTAAGGATA 1 127 0 GATTTTATCT 0.991688 -174 GCTGTCGGGCTATTTCGTAGATCCTGAGTTTGTTA 1 142 0 TATTTAATCT 0.913252 -159 AAAAATCTTCGAACTGTTTATTCGTTGGAGCAAAA 1 276 1 GACTTTTTCT 0.9228 -25 GCATAATTGCTGGTTATTTTATCTTCCCCGAGGGG 2 28 1 TGTTTTATCT 0.945884 -96 ACTTACCGCCTATTTTATTTAACCTAAATTTTGTT 2 99 1 TATTTTAACT 0.954119 -25 TTCTATGCGTTAATTTTTTTATCATTCGGAAGAAT 3 37 1 TATTTTATCT 0.986811 -26 TATTGATCTTGATTTAATTAAACGTTTTGACCTAG 5 112 0 GATTTTAACT 0.970727 -48 CTTCTGTTTTGATCTTATTGATCTTGATTTAATTA 5 127 0 GACTTTATCT 0.988365 -33 ** ** ** *** * Masking position 8 Map Score: 10.0657 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 135 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 CATCAACTACTAATAGCCAGTGCTACTTTTC 1 38 1 TAATAGCCGT 0.979567 -263 TCATTATTCTACTTTGCCTGTTATTGAAAAG 1 63 0 ACTTTGCCGT 0.916583 -238 AGGATCTACGAAATAGCCCGACAGCGGCAAC 1 152 1 AAATAGCCGA 0.959865 -149 ATATGATATCACAAAGCCTGTATTTTTTAAC 1 230 1 ACAAAGCCGT 0.964441 -71 TTTTTAAACAAAAAAGCCTGTTAAAAAATAC 1 249 0 AAAAAGCCGT 0.979561 -52 AGGTTAAATAAAATAGGCGGTAAGTCTAGTT 2 93 0 AAATAGGCGT 0.956603 -31 TGGGTAATTAAATTACCCATTTATTGCATCA 4 11 0 AATTACCCTT 0.925887 -36 TGGGTAATTTAATTACCCATTTTTTATAGAA 4 23 1 AATTACCCTT 0.925887 -24 TTAGTAAAAGTGTTACCCCGTTGGGAGTGGA 5 64 0 TGTTACCCGT 0.860539 -96 ******** ** Masking position 8 Map Score: 6.33409 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 224 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 GTCATATTTTTATCCTTAGTATGATTAACA 1 117 1 TATCCTTAGT 0.939489 -184 CTATTTTATTTAACCTAAATTTTGTT 2 108 1 TAACCTAAAT 0.908037 -16 AGGCTAGGTATAGCCTAGGTTAGTAAAAGT 5 84 0 TAGCCTAGGT 0.993995 -76 AGGCTATACCTAGCCTAGGTCAAAACGTTT 5 98 1 TAGCCTAGGT 0.993995 -62 ********** Masking position 6 Map Score: 1.16986 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 4 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 CATACTAAGGATAAAAATATGACTAAATTT 1 110 0 ATAAAAATAT 0.815523 -191 TCAAAGAGCATTGAAAATATGATATCACAA 1 214 1 TTGAAAATAT 0.884409 -87 AAAAAAGCCTGTTAAAAAATACAGGCTTTG 1 241 0 GTTAAAAAAT 0.886314 -60 GGCTTTTTTGTTTAAAAAATCTTCGAACTG 1 262 1 TTTAAAAAAT 0.930023 -39 CCCCTCGGGGAAGATAAAATAACCAGCAAT 2 33 0 AAGATAAAAT 0.752474 -91 AAATGATCTCAAGAAAAAATCTCCCCTCGG 2 55 0 AAGAAAAAAT 0.944333 -69 CTTCCGAATGATAAAAAAATTAACGCATAG 3 39 0 ATAAAAAAAT 0.923484 -24 AATTTCTATAAAAAATGGGTAATTAA 4 31 0 TATAAAAAAT 0.892303 -16 ********** Masking position 6 Map Score: 4.30163 Number of sites scoring better than the average of aligned sites = 824 Number in coding regions = 578 Number in noncoding regions = 246 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 5 TAATAGCCAGTGCTACTTTTCAATAACAGG 1 48 1 TGCTACTTTT 0.824497 -253 GTCATCATTATTCTACTTTGCCTGTTATTG 1 68 0 TTCTACTTTG 0.967734 -233 GCCGCTGTCGGGCTATTTCGTAGATCCTGA 1 150 0 GGCTATTTCG 0.941972 -151 TTTTTTAACAGGCTTTTTTGTTTAAAAAAT 1 252 1 GGCTTTTTTG 0.941298 -49 TAGGCGGTAAGTCTAGTTTGAATTGAAAAT 2 81 0 GTCTAGTTTG 0.951645 -43 GTGATAGCGGTTCTCTTTTGGGAAAAGCTA 5 32 1 TTCTCTTTTG 0.942187 -128 TTTATTTCCTTCTGTTTTGATCTTATTGA 5 141 0 TTCTGTTTTG 0.942187 -19 ********** Masking position 4 Map Score: 2.96718 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 154 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 ********** No masking Map Score: 6.98764e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 ********** No masking Map Score: 6.98764e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: 6.98764e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0